Edit Mode: disable closest selection
Not really an answer as there is currently no solution to my specific problem in 2.79. But I did find some alternative to de-selection.

I have created a keymap based on the 2.80 "Industry Standard Keymap" proposal in case people ran into the same issue as me.

https://gist.github.com/bitinn/22f6fefe026d8d9e83468864edb8f835